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The effects of habitat fragmentation and the resulting decreases in effective population sizes are not easy to document because they take place over many generations and may be affected by factors other than demographic ones. Here, we used 22 microsatellite loci to investigate genetic structure and diversity in populations of edible dormice Glis glis from habitats that varied widely in area and in the degree of connectivity to other populations. We found that populations from the most fragmented north-western region of Poland were characterized by extremely limited gene flow and low genetic diversity compared to less fragmented populations from southern Poland. STRUCTURE analysis revealed three genetic groups in Poland, which might reflect adaptation to environmental conditions across south-north and east-west gradients, but could also be due to historical patterns of post-glacial colonization. The latter hypothesis is suggested by the observation that southern populations from Poland grouped with those from the Balkans based on microsatellite data; however, the fact that all Polish populations shared western mt DNA cytochrome b haplotypes is inconsistent with this scenario. We discuss the consequences of our findings for the conservation of the edible dormouse in Poland. [ABSTRACT FROM AUTHOR]